kmerPyramid: an interactive visualization tool for nucleobase and k-mer frequencies

Jochen Kruppa; Erhard van der Vries; Wendy K Jo; Alexander Postel; Paul Becher; Albert Osterhaus; Klaus Jung

doi:10.1093/bioinformatics/btx385

kmerPyramid: an interactive visualization tool for nucleobase and k-mer frequencies

Jochen Kruppa, Erhard van der Vries, Wendy K Jo, Alexander Postel, Paul Becher, Albert Osterhaus, Klaus Jung

Research output: Contribution to journal › Article › Academic › peer-review

Abstract

Summary: Bioinformatics methods often incorporate the frequency distribution of nulecobases or k-mers in DNA or RNA sequences, for example as part of metagenomic or phylogenetic analysis. Because the frequency matrix with sequences in the rows and nucleobases in the columns is multi-dimensional it is hard to visualize. We present the R-package 'kmerPyramid' that allows to display each sequence, based on its nucleobase or k-mer distribution projected to the space of principal components, as a point within a 3-dimensional, interactive pyramid. Using the computer mouse, the user can turn the pyramid's axes, zoom in and out and identify individual points. Additionally, the package provides the k-mer frequency matrices of about 2000 bacteria and 5000 virus reference sequences calculated from the NCBI RefSeq genbank. The 'kmerPyramid' can particularly be used for visualization of intra- and inter species differences.

Availability and implementation: The R-package 'kmerPyramid' is available from the GitHub website at https://github.com/jkruppa/kmerPyramid.

Contact: [email protected].

Supplementary information: Supplementary data are available at Bioinformatics online.

Original language	English
Pages (from-to)	3115-3116
Number of pages	2
Journal	Bioinformatics
Volume	33
Issue number	19
DOIs	https://doi.org/10.1093/bioinformatics/btx385
Publication status	Published - 1 Oct 2017
Externally published	Yes

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title = "kmerPyramid: an interactive visualization tool for nucleobase and k-mer frequencies",

abstract = "Summary: Bioinformatics methods often incorporate the frequency distribution of nulecobases or k-mers in DNA or RNA sequences, for example as part of metagenomic or phylogenetic analysis. Because the frequency matrix with sequences in the rows and nucleobases in the columns is multi-dimensional it is hard to visualize. We present the R-package 'kmerPyramid' that allows to display each sequence, based on its nucleobase or k-mer distribution projected to the space of principal components, as a point within a 3-dimensional, interactive pyramid. Using the computer mouse, the user can turn the pyramid's axes, zoom in and out and identify individual points. Additionally, the package provides the k-mer frequency matrices of about 2000 bacteria and 5000 virus reference sequences calculated from the NCBI RefSeq genbank. The 'kmerPyramid' can particularly be used for visualization of intra- and inter species differences.Availability and implementation: The R-package 'kmerPyramid' is available from the GitHub website at https://github.com/jkruppa/kmerPyramid.Contact: [email protected] information: Supplementary data are available at Bioinformatics online.",

author = "Jochen Kruppa and {van der Vries}, Erhard and Jo, {Wendy K} and Alexander Postel and Paul Becher and Albert Osterhaus and Klaus Jung",

year = "2017",

month = oct,

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doi = "10.1093/bioinformatics/btx385",

language = "English",

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AU - Kruppa, Jochen

AU - van der Vries, Erhard

AU - Jo, Wendy K

AU - Postel, Alexander

AU - Becher, Paul

AU - Osterhaus, Albert

AU - Jung, Klaus

PY - 2017/10/1

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N2 - Summary: Bioinformatics methods often incorporate the frequency distribution of nulecobases or k-mers in DNA or RNA sequences, for example as part of metagenomic or phylogenetic analysis. Because the frequency matrix with sequences in the rows and nucleobases in the columns is multi-dimensional it is hard to visualize. We present the R-package 'kmerPyramid' that allows to display each sequence, based on its nucleobase or k-mer distribution projected to the space of principal components, as a point within a 3-dimensional, interactive pyramid. Using the computer mouse, the user can turn the pyramid's axes, zoom in and out and identify individual points. Additionally, the package provides the k-mer frequency matrices of about 2000 bacteria and 5000 virus reference sequences calculated from the NCBI RefSeq genbank. The 'kmerPyramid' can particularly be used for visualization of intra- and inter species differences.Availability and implementation: The R-package 'kmerPyramid' is available from the GitHub website at https://github.com/jkruppa/kmerPyramid.Contact: [email protected] information: Supplementary data are available at Bioinformatics online.

AB - Summary: Bioinformatics methods often incorporate the frequency distribution of nulecobases or k-mers in DNA or RNA sequences, for example as part of metagenomic or phylogenetic analysis. Because the frequency matrix with sequences in the rows and nucleobases in the columns is multi-dimensional it is hard to visualize. We present the R-package 'kmerPyramid' that allows to display each sequence, based on its nucleobase or k-mer distribution projected to the space of principal components, as a point within a 3-dimensional, interactive pyramid. Using the computer mouse, the user can turn the pyramid's axes, zoom in and out and identify individual points. Additionally, the package provides the k-mer frequency matrices of about 2000 bacteria and 5000 virus reference sequences calculated from the NCBI RefSeq genbank. The 'kmerPyramid' can particularly be used for visualization of intra- and inter species differences.Availability and implementation: The R-package 'kmerPyramid' is available from the GitHub website at https://github.com/jkruppa/kmerPyramid.Contact: [email protected] information: Supplementary data are available at Bioinformatics online.

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JO - Bioinformatics

JF - Bioinformatics

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ER -

kmerPyramid: an interactive visualization tool for nucleobase and k-mer frequencies

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